Table 1. Overview of MD data
MD runSimulation time (µs)Applied electric field (mV)Ion sites occupied at starting stateHBC gate permeation events
200ns_run10.2S2, S40
200ns_run20.2S2, S40
200ns_run30.2S2, S40
200ns_run40.2S2, S40
200ns_run50.2S2, S40
200ns_run60.2S2, S41
200ns_run70.2S2, S41
200ns_run80.2S2, S41
200ns_run90.2S2, S40
200ns_run100.2S2, S40
Full SF permeation events
1µs_run11580S1, S2, S430
1µs_run21580S1, S2, S49
1µs_run31580S1, S2, S40
1µs_run41580S2, S38
1µs_run51580S2, S327
1µs_run61580S2, S320
1µs_run71580S2, S315
1µs_run8a1580S2, S324
1µs_run9a1580S2, S319
1µs_run10a1580S2, S327
1µs_run111290S2, S30
1µs_run121290S2, S319
1µs_run13a1290S2, S327
1µs_run14a1290S2, S33
Total number16228

10 replicas of 0.2-µs free MD simulations were performed using the equilibrated system of the crystal structure with bound PIP2 (PDB accession no. 3SYA). 14 1-µs simulations were performed with an applied electric field. 1µs_run1, 1µs_run2 and 1µs_run3 started from a snapshot at 50ns of 200ns_run8. All the other MD runs with applied electric field were initiated from a snapshot of 1µs_run1 (t = 400 ns), where the HBC gate reached a steady state of a relatively wide and solvated conformation (see Figs. S4 and S5 B). For all 1-µs simulations, either 40 mV nm−1 or 20 mV nm−1 was applied; this equals ∼580 mV or ∼290 mV, respectively, when calculated over the whole box (z axis; Roux, 2008; Bjelkmar et al., 2009; Gumbart et al., 2012).

  • a Harmonic restraints on G-loop gate–forming residues G318 and M319.